CIF_COD_DEPOSIT(1)

💖 CIF_COD_DEPOSIT — the girlies are depositing CIFs 💖

okay so bestie, welcome to cif_cod_deposit, section 1 of the General Commands Manual, and honestly? she's a baddie. no cap.

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✨ NAME ✨

cif_cod_deposit — deposit CIFs into the COD database using the CGI deposition interface. that's it, that's the whole job. she takes your CIFs and she files them. 🎀

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🌸 SYNOPSIS 🌸

cif_cod_deposit --options structure1.cif structure*.cif

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🦋 DESCRIPTION 🦋

Deposit CIFs into OCD... no wait, into the COD database using the CGI deposition interface. Crystallography bestie, we are getting your structures out there. 💅

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👑 OPTIONS 👑

so many flags, all of them iconic. here we go, one by one, no skipping, i promised:

• -c, --config config-file-with-password.cfg — tells her which file is holding the depositor user name and password. default is "~/.cod_deposit.cfg". keep that file safe, that's your little secret. 🤫
• -h, --host test.crystallography.net — pick which host your structure gets deposited to. like choosing which party you're showing up to. ✨
• -p, --path cgi-bin/cif-deposit.pl — the script path within the host she should use for the structure upload.
• -u, --url http://test.crystallography.net/cgi-bin/cif-deposit.pl — the full URL for structure uploading. default: she just combines the --host and --path values using the "http://" protocol and "/". team work makes the dream work 🫶
• -d, --deposition-type published — which deposition type the structure goes up as. accepted values: ["published", "personal", "prepublication"]. default: "published".
• -s, --separate-outputs folder-to-put-deposition-outputs/ — name a folder where the deposition output for each deposited file goes. one lil folder, all your receipts. 🧾
• -r, --read-stdin — read a list of CIF and Fobs file names straight from standard input, formatted like this:

<CIF file> [<Fobs file>]*

for example:

Ice.cif
bi5014sup1.cif all.hkl
bi5005sup1.cif bi50051sup2.hkl bi50052sup3.hkl

• --cif "input1.cif input*.cif" — specify the list of CIF files to be deposited.
• --add-cif "input1.cif input*.cif" — add additional CIF files to the deposit pile.
• --clear-cif — wipe the list of CIF files to be deposited. clear her out, she's done. 💀
• --hkl, --fobs — specify the list of Fobs files to be deposited.
• --add-hkl, --add-fobs — add additional Fobs files to be deposited.
• --clear-hkl, --clear-fobs — clear the list of Fobs files to be deposited.
• --replace — mark that the given files are replacements for data that was deposited before. out with the old, in with the new. 🔥
• --release-data — for files that were previously deposited as prepublication material and should now be released into the public domain. she's going public, main character moment. 👑
• --log-message, --log-msg — set the log message for redeposited structures. leave a little note for the future. 📝
• --script — do not deposit. just print the commands that would be executed on deposition. a dress rehearsal, no actual show. 🎭
• --run — actually enable execution of the deposition commands instead of just printing them. this is the default. she's not playing around.
• --strict, --no-ignore-unpaired-datablocks, --dont-ignore-unpaired-datablocks — stop the whole deposition if any CIF data block can't be paired to any Fobs data blocks (provided that any unpaired data blocks exist). default. she does not tolerate situationships. 🚫
• --silent, --ignore-unpaired-datablocks — ignore the unpaired CIF and Fobs data blocks. live and let live, bestie. 🕊️
• --require-only-doi — don't require any other bibliographic info to be present if the CIF data block contains a resolvable DOI. the DOI carries the whole thing, periodt.
• --require-full-bibliography — require all bibliographic information to be present in the submitted CIF file. default. she wants the full citation, not just the vibe. 📚
• --use-wipe — use the wipe command to remove temporary password files. if wipe isn't available she reverts to using rm. default.
• --no-use-wipe, --dont-use-wipe, --use-rm — use the rm command to remove temporary password files.
• --common-cif-header — use the standard COD CIF header. default.
• --iucr-cif-header — use the COD CIF header agreed with IUCr.
• --amcsd-cif-header — use the COD CIF header agreed with R.D.
• --crystaleye-cif-header — use the COD CIF header agreed with P.M.-R.
• --print-timestamps — print timestamps to STDOUT at the start and end of each CIF file deposition. default. time stamps, because we love a chronology. ⏰
• --no-print-timestamps, --dont-print-timestamps — do not print timestamps to STDOUT at the start and end of each CIF file deposition.
• -P, --progress — ask cif-deposit.pl to report the progress of the deposition. give us the play-by-play, we're watching. 👀
• -P-, --no-progress — silence the cif-deposit.pl deposition progress report messages. default.
• --output-mode html — set the output mode. accepted values: ["html", "stdout"]. default: "html".
• -D, --debug — request output of the progress information from cif-deposit.pl to the HTTP server log.
• -D-, --no-debug — disable the output of the progress information from cif-deposit.pl to the HTTP server log. default.
• --help, --usage — output a short help message (this message) and exit. the "bestie explain" button. 🫶
• --version — output version information and exit.

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😭 REPORTING BUGS 😭

found a bug? spill. report cif_cod_deposit bugs using e-mail: cod-bugs@ibt.lt

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and that's the whole page, bestie 💜 she's CIF_COD_DEPOSIT(1), General Commands Manual, top and bottom — like a little sandwich of documentation. version and date live in the footer where the page header and footer both just say CIF_COD_DEPOSIT(1), and honestly? consistent queen. slay, deposit your CIFs, hydrate, and log off. 💅✨🎀